Category Archives: Bik’s Non-Microbiology Picks

December 28, 2014

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Human oral microbiome

Periodontitis: from microbial immune subversion to systemic inflammation – George Hajishengallis – Nature Reviews Immunology

Microbiology of Oral Biofilm-Dependent Diseases: Have We Made Significant Progress to Understand and Treat These Diseases? – Ana Paula Vieira Colombo – Current Oral Health Reports

Human skin microbiome

Dynamics of the surgical microbiota along the cardiothoracic surgery pathway – Sara Romano-Bertrand – Frontiers in Microbiology

Human gut microbiome

Decreased Bacterial Diversity Characterizes the Altered Gut Microbiota in Patients With Psoriatic Arthritis, Resembling Dysbiosis in Inflammatory Bowel Disease – Jose U. Scher – Arthritis & Rheumatology

Insights Into the Role of the Microbiome in Obesity and Type 2 Diabetes – Annick V. Hartstra – Diabetes Care

* The gut microbiota and its role in the development of allergic disease: a wider perspective – C. E. West – Clinical & Experimental Allergy

The power in numbers: Gut microbiota in Parkinson’s disease – Joaquin A. Vizcarra – Movement Disorders

Childhood Obesity: A Role for Gut Microbiota? – Marina Sanchez – Int. J. Environ. Res. Public Health

Animal models of microbiome

Impact of the gut microbiota on rodent models of human disease – Axel Kornerup Hansen – World Journal of Gastroenterology

Dynamics and Establishment of Clostridium difficile Infection in the Murine Gastrointestinal Tract – Mark J. Koenigsknecht – Infection and Immunity

Alteration of the fecal microbiota and serum metabolite profiles in dogs with idiopathic inflammatory bowel disease – Yasushi Minamoto – Gut Microbes

Intermittent hypoxia alters gut microbiota diversity in a mouse model of sleep apnoea
Isabel Moreno-Indias – European Respiratory Journal

Bioreactor models

Lead toxicity to the performance, viability, and community composition of activated sludge microorganisms – Husen Zhang – Environmental Science & Technology

Animal microbiome

Diet strongly influences the gut microbiota of surgeonfishes – Sou Miyake – Molecular Ecology

Plant microbiome

21st century agriculture: integration of plant microbiomes for improved crop production and food security – Angela Sessitsch and Birgit Mitter – Microbial Biotechnology

Soil microbiome

Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield – Thomas Rime – Molecular Ecology

Changes in the composition and diversity of bacterial communities 13 years after soil reclamation of abandoned mine land in eastern China – Yuanyuan Li – Ecological Research

Nitrogen cycling processes and microbial community composition in bed sediments in the Yukon River at Pilot Station – Deborah A. Repert – Journal of Geophysical Research: Biogeosciences

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation – Annelie Steinbach – ISME Journal

Different vegetable crop rotations affect soil microbial communities and soilborne diseases of potato and onion: literature review and a long-term field evaluation – PJ Wright – New Zealand Journal of Crop and Horticultural Science

Water microbiome

* Biogeography and ecology of the rare and abundant microbial lineages in deep-sea – Rika E. Anderson – FEMS Microbiology Ecology

Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage – Lin-xing Chen – ISME Journal

Microbes of the built environment

Indoor bioaerosol dynamics – William W Nazaroff – Indoor Air

Bioinformatics

An improved method to set significance thresholds for β diversity testing in microbial community comparisons – Arda Gülay and Barth F. Smets – Environmental Microbiology

Metabolomics

Reevaluating the hype: Four bacterial metabolites under scrutiny – Esther Eleonore Fröhlich – European Journal of Microbiology and Immunology

Microbes in the news

Discovering microbiology – Nicholas P Money – Oxford University Press

The Microbes in Your Kitchen (Or in your Starbucks mocha) – Kevin Bonham – Scientific American

Science, Publishing, Career

Science is the most ‘future proof’ degree: Engineering and chemistry seen as courses likely to lead to an adaptable career – Laura Clark – Daily Mail

Bik’s Picks

Dr. Oz gets roasted in science journal’s Christmas edition — science roundup extra (video, links) – Susannah L. Bodman – Oregon Live

Science Explains Why The Best BBQ Is Slow Cooked – Patrick Allan – LifeHacker

The Shapes of Snowflakes – CompoundChem

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December 23, 2014

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Microbiome publications are definitely not taking a winter break, so here is your holiday update. Merry Christmas to those who celebrate!

Human oral microbiome

Serum IgG Antibody Levels to Periodontal Microbiota Are Associated with Incident Alzheimer Disease – James M. Noble – PLOS ONE

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle – Xuesong He – PNAS USA

Pyrosequencing of supra- and subgingival biofilms from inflamed peri-implant
and periodontal sites – Simone Schaumann – BMC Oral Health

Human respiratory microbiome

The Microbial Community of the Cystic Fibrosis Airway Is Disrupted in Early Life – Julie Renwick – PLOS ONE

Human gut or general microbiome
Effects of bowel cleansing on the intestinal microbiota – Jonna Jalanka – Gut

The Microbiome of Aging and Age-Related Disease – 2014 Meeting Abstracts

Microbial community pattern detection in human body habitats via ensemble clustering framework – Peng Yang – ArXiv.org

Cancer and the microbiome: potential applications as new tumor biomarker – Khan Shahanavaj – Expert Review of Anticancer Therapy

Influence of Intestinal Microbiota on Body Weight Gain: a Narrative Review of the Literature – Camila S. Cardinelli – Obesity Surgery

Animal models of microbiome research

Host genetics and diet, but not immunoglobulin A expression, converge to shape
compositional features of the gut microbiome in an advanced intercross population
of mice – Larry J Leamy – Genome Biology

Animal microbiome

Microbiomes, plausible players or not in alteration of host behaviour – David G. Biron – Frontiers in Microbiology

The Howler Monkey as a Model for Exploring Host-Gut Microbiota Interactions in Primates – Katherine R. Amato, Nicoletta Righini – Howler Monkeys

The Gut Microbiota Appears to Compensate for Seasonal Diet Variation in the Wild Black Howler Monkey (Alouatta pigra) – Katherine R. Amato – Microbial Ecology

Application of the Human Intestinal Tract Chip to the non-human primate gut microbiota – T.D.J. Bello González – Beneficial Microbes

Effects of dietary supplementation of a commercial prebiotic Previda® on survival, growth, immune responses and gut microbiota of Pacific white shrimp, Litopenaeus vannamei – J.D. Anuta – Aquaculture Nutrition

Metagenomic-Based Study of the Phylogenetic and Functional Gene Diversity in Galápagos Land and Marine Iguanas – Pei-Ying Hong – Microbial Ecology

Plant microbiome

The plant microbiome at work – Klaus Schlaeppi and Davide Bulgarelli – Molecular Plant-Microbe Interactions

Tree communities rapidly alter soil microbial resistance and resilience to drought – David Rivest – Functional Ecology

The Sesquiterpene Biosynthesis and Vessel-Occlusion Formation in Stems of Aquilaria sinensis (Lour.) Gilg Trees Induced by Wounding Treatments without Variation of Microbial Communities – Zheng Zhang – International Journal of Molecular Sciences

Analysis of microbial taxonomical groups present in maize stalks suppressive to colonization by toxigenic Fusarium spp.: A strategy for the identification of potential antagonists – Jürgen Köhl – Biological Control

Soil and sediment microbiome

Diversity, Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland – Raeid M. M. Abed – PLOS ONE

Do climate factors govern soil microbial community composition and biomass at a regional scale? – L. Ma – Biogeosciences Discuss

Water microbiome

Early succession of micro-periphyton communities in kelp bed and barren ground ecological systems – Roberto A. Uribe – Marine Ecology

Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China – Shang Wang – Scientific Reports

Effects of warming on microbial communities in the coastal waters of temperate and subtropical zones in the Northern Hemisphere, with a focus on Gammaproteobacteria
Dao Thi Anh Tuyet – Journal of Oceanography

Colonization in the photic zone and subsequent changes during sinking determines bacterial community composition in marine snow – Stefan Thiele – Applied and Environmental Microbiology

Diversity, Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland
Raeid M. M. Abed – PLOS ONE

Bioreactor microbiology

Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures – Shaobo Liang – Bioresource Technology

A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates – Damian E. Helbling – Water Research

Metagenomics

Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India – Johan Bengtsson-Palme – Frontiers in Microbiology

Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity – Michelle Davison – Photosynthesis Research

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms – Martial Marbouty – eLIFE

Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing – Alexander W. Eastman and Ze-Chun Yuan – Frontiers in Microbiology

Metabolomics and transcriptomics

Terpene synthases are widely distributed in bacteria – Yuuki Yamada – PNAS USA

Scaling microbial biomass, metabolism and resource supply – Robert L. Sinsabaugh – Biogeochemistry

Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume – Jason A Hilton – ISME Journal

Mining Soil Metagenomes to Better Understand the Evolution of Natural Product Structural Diversity: Pentangular Polyphenols as a Case Study – Hahk-Soo Kang and Sean F. Brady – Journal of the American Chemical Society

Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale – Darrell W. Cockburn – Molecular Microbiology

Techniques

Deciphering the Prokaryotic Community and Metabolisms in South African Deep-Mine Biofilms through Antibody Microarrays and Graph Theory – Yolanda Blanco – PLOS ONE

Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing – Annette Carola Anderson – BMC Microbiology

Probiotics

Probiotic and technological properties of Lactobacillus spp. strains from the human stomach in the search for potential candidates against gastric microbial dysbiosis – Susana Delgado – Frontiers in Microbiology

Phages and viruses

Effectiveness of bacteriophages in the sputum of cystic fibrosis patients – E. Saussereau – Clinical Microbiology and Infection

More Microbiology

Bridging the gap between viable but non-culturable and antibiotic persistent bacteria – Mesrop Ayrapetyan – Trends in Microbiology

Bacterial microcompartments and the modular construction of microbial metabolism – Cheryl A. Kerfeldemail, Onur Erbilgin – Trends in Microbiology

The impact of triclosan on the spread of antibiotic resistance in the environment – Daniel E. Carey – Frontiers in Microbiology

Microbes in the news

At Last, I Meet My Microbes – Katherine Harmon Courage – NPR Shots

This Is Your Microbiome: Katherine Harmon Courage at NPR is taking a tour through her microbiome and that of her husband, mother, and dog, as she recounts in a four-part series – Genome Web

Big Idea 2015: Medicine, Wellbeing, and the Microbiome – Deepak Chopra – LinkedIn

When Threatened By Worms, Bacteria Summon Killer Fungi – Ed Yong – National Geographic

Parkinson’s disease linked to gut bacteria – Tim Sandle – Digital Journal

Bacteria in 550-million-year-old fossils provide new clues about fossil formation – Science Codex

Yellowstone Thermal Pools Colored by Pollution – Patrick J Kiger – Discovery

Floating Toilets That Clean Themselves Grow On A Lake – Nsikan Akpan – NPR Goats and Soda

Bettendorf wrestling coach’s invention tackles germs and bacteria on sporting mats and floors – Dennis Moran – QC Online

People on Craigslist Want to Give You Bacteria for Free – Natalie Kitroeff – BusinessWeek

Science, publishing, career

Patterns of text reuse in a scientific corpus – Daniel T. Citron and Paul Ginsparg – PNAS USA

The Anti-Plagiarism Machine: An analysis of hundreds of thousands of scientific papers finds text re-use is rampant, but it isn’t always malicious – Adrienne Lafrance – The Atlantic

“You Are Welcome Here”: Small Stickers Make a Big Difference for LGBTQ Scientists – Kyle Frischkorn – Scientific American

Science and Art

Incredible Bacteria-Laced Fabric Combines Art, Biology And Fashion – Priscilla Frank – Huffington Post
Bik’s Picks

Evolutionary perspectives on human height variation – Gert Stulp and Louise Barrett – Biological Reviews

What the ‘marshmallow test’ can teach you about your kids – Chuck Hadad – CNN

7 of the Ocean’s Strangest Creatures, Including a Fish With a Flashlight – Matt Simon – Wired

Modern genetics confirm ancient relationship between fins and hands – Science Daily

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December 19, 2014

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Pregnancy and Birth

Lots of abstracts (mostly from the group of Kjersti Aagaard) from the 35th Annual Meeting of the Society for Maternal-Fetal Medicine — The Pregnancy Meeting in the American Journal of Obstetrics and Gynecology

13: Association of preterm birth with alterations in the microbiome and linkage to host mtDNA variants – Kjersti Aagaard

57: Alterations in the intestinal microbiome of infants are associated with breastfeeding practice – Derrick Chu

78: Distinct alterations in the placental microbiome among spontaneous preterm births – Kjersti Aagaard

79: Metagenomics of a population-based prospective cohort reveals no discernable impact of mode of delivery (MOD) on the infant microbiome by 6 weeks of age – Derrick Chu

122: The microbiome of the placenta is altered among subjects with severe chorioamnionitis & spontaneous preterm birth – Amanda Prince

282: Chorioamnionitis induced by intramniotic injection of IL1, LPS or Ureaplasma parvum is associated with an altered microbiome in a primate model of inflammatory preterm birth (PTB) – Amanda Prince

283: Amniotic fluid microbiome community and inflammation in women with second trimester cervical changes – Amanda Roman

342: Poor maternal nutrition is associated with alterations in the maternal and neonatal microbiome communities – Kathleen Antony

650: Characterization of the vaginal microbiome following preterm premature rupture of membranes (PPROM) – Janet Hill

709: Race, latency, and fetal membrane microbiota diversity in preterm premature rupture of membranes – Sarahn Wheeler

Human oral microbiome

* Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa – Li J – BMC Microbiology

Human respiratory microbiome

* The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition – Cremers AJ – Microbiome Journal

Human gut microbiome

* The gut microbiota of Colombians differs from that of Americans, Europeans and Asians – Escobar JS – BMC Microbiology

Gut Microbiota: Its Role in Hepatic Encephalopathy – Rahul Rai – Journal of Clinical and Experimental Hepatology

The fungal microbiota of de-novo paediatric inflammatory bowel disease – I. Mukhopadhya – Microbes and Infection

Human vaginal microbiome

Colonization of the upper genital tract by vaginal bacterial species in non-pregnant women  – Caroline M. Mitchell – American Journal of Obstetrics and Gynecology

Transcriptional fingerprints of antigen-presenting cell subsets in the human vaginal mucosa and skin reflect tissue-specific immune microenvironments – Dorothée Duluc – Genome Medicine

Animal models

Microbially Driven TLR5-Dependent Signaling Governs Distal Malignant Progression through Tumor-Promoting Inflammation – Melanie R. Rutkowski – Cancer Cell

Intestinal microbiota diversity and expression of pattern recognition receptors in newly weaned piglets – Xin Tao – Anaerobe

Host genetics and diet, but not immunoglobulin A expression, converge to shape
compositional features of the gut microbiome in an advanced intercross population
of mice – Larry J Leamy – Genome Biology

The effects of Lactobacillus acidophilus as feed supplement on skin mucosal immune parameters, intestinal microbiota, stress resistance and growth performance of black swordtail (Xiphophorus helleri) – Seyed Hossein Hoseinifar – Fish & Shellfish Immunology

Animal microbiome

Investigation of a new acetogen isolated from an enrichment of the tammar wallaby forestomach – Gagen EJ – BMC Microbiology

Metagenomics, bioinformatics

Determining the quality and complexityof next-generation sequencing data without
a reference genome – Seyed Yahya Anvar – Genome Biology

Techniques

Tracking down the sources of experimental contamination in microbiome studies – Sophie Weiss – Genome Biology

More microbiology

Single cell genomics of bacterial pathogens: outlook for infectious disease research – Jeffrey S McLean and Roger S Lasken – Genome Medicine

A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens – Maha R Farhat – Genome Medicine

Environmental enteropathy and malnutrition: do we know enough to intervene? – William A Petri – BMC Medicine

Microbes in the news

Mix of Bacteria in Gut May Depend More on Diet than Genes – Microbiota, Microbiome Change Quickly, UCSF Researchers Find – Jeffrey Norris – UCSF

Protection of the mouse gut by mucus depends on microbes – Phys.org

Life would go on if all bacteria disappeared (but it would totally suck) – Rachel Feltman – Washington Post

New technology using bacteria from dung helps coffee farmers to purify water – Oliver Balch – The Guardian

Science, publishing, career

Dragging scientific publishing into the 21st century – Razib Khan – Genome Biology

Training for peer review: why we need it and how to get there – David Moher – Biome BioMedCentral

Along with the privilege of authorship come important responsibilities – David Moher – BMC Medicine

Crashing the Old Boys’ Science Club – Yamina Berchiche – Live Science

Bik’s Picks

‘People Can Be Afraid of Anything’ – There are plenty of people afraid of whales who will never even see one. How I learned about, and tried to conquer, my own cetaphobia – Kate Horowitz – The Atlantic

Playlist: Science! – NPR/TED staff – NPR

Birds sensed severe storms and fled before tornado outbreak – Science Daily

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December 16, 2014

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Pregnancy and birth

* The establishment of the infant intestinal microbiome is not affected by rotavirus vaccination – Li Ang – Scientific Reports

In pregnant women: Gut Microbiota as an Epigenetic Regulator: Pilot Study Based on Whole-Genome Methylation Analysis – Himanshu Kumar – mBio

Human skin and hair microbiome

* Molecular characterization of the skin fungal microbiome in patients with psoriasis – Akemi Takemoto – The Journal of Dermatology

* Metagenomic analyses of bacteria on human hairs: a qualitative assessment for applications in forensic science – Silvana R Tridico – Investigative Genetics

Human oral microbiome

Oral Streptococci and Nitrite-Mediated Interference of Pseudomonas aeruginosa – Jessica A. Scoffield and Hui Wu – Infection and Immunity

Antimicrobial effect of lemongrass oil against oral malodour micro-organisms and the pilot study of safety and efficacy of lemongrass mouthrinse on oral malodour – P. Satthanakul – Journal of Applied Microbiology

Human respiratory microbiome

The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition – Amelieke JH Cremers – Microbiome Journal

Human gut microbiome

Shaping the gut microbiome – Linda Koch – Nature Reviews Microbiology

A viral understudy for commensal bacteria – Yvonne Bordon – Nature Reviews Microbiology

* Impacts of infection with different toxigenic Clostridium difficile strains on faecal microbiota in children – Zongxin Ling – Scientific Reports

Gut Microbiota as an Epigenetic Regulator: Pilot Study Based on Whole-Genome Methylation Analysis – Himanshu Kumar – mBio

Dietary effects on human gut microbiome diversity – Zhenjiang Xua and Rob Knight – British Journal of Nutrition

Host Demise as a Beneficial Function of Indigenous Microbiota in Human Hosts – Martin J. Blaser and Glenn F. Webb – mBio

Editorial for special issue of CMI: Faecal transplantation and infectious diseases practitioners – D. Raoult – Clinical Microbiology and Infection

Review: Dysbiotic Events in Gut Microbiota: Impact on Human Health – Serena Schippa and Maria Pia Conte – Nutrients

Animal and other models of microbiome research

A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation – Robert A Quinn – ISME Journal

Whole Grain Oats Improve Insulin Sensitivity and Plasma Cholesterol Profile and Modify Gut Microbiota Composition in C57BL/6J Mice – Albert Lihong Zhou – Journal of Nutrition

The Antipsychotic Olanzapine Interacts with the Gut Microbiome to Cause Weight Gain in Mouse – Andrew P. Morgan – PLOS ONE

Genetically identical co-housed pigs as models for dietary studies of gut microbiomes –
Fang Yang – Microbiome Science and Medicine

Animal microbiome

Changes in the faecal microbiota of mares precede the development of post partum colic – J. S. Weese – Equine Veterinary Journal

Succession and Replacement of Bacterial Populations in the Caecum of Egg Laying Hens over Their Whole Life – Petra Videnska – PLOS ONE

 

* Adult blood-feeding tsetse flies, trypanosomes, microbiota and the fluctuating environment in sub-Saharan Africa – Anne Geiger – ISME Journal

Spatial and Temporal Features of the Growth of a Bacterial Species Colonizing the Zebrafish Gut – Matthew Jemielita – mBio

Functional genomics and microbiome profiling of the Asian longhorned beetle (Anoplophora glabripennis) reveal insights into the digestive physiology and nutritional ecology of wood feeding beetles – Erin D Scully – BMC Genomics

 

Bacteria–bacteria interactions within the microbiota of the ancestral metazoan Hydra contribute to fungal resistance – Sebastian Fraune – ISME Journal

Plant microbiome

Local-scale biogeography and spatiotemporal variability in communities of mycorrhizal fungi – Mohammad Bahram – New Phytologist

Emergence shapes the structure of the seed-microbiota – Matthieu Barret – Applied and Environmental Microbiology

Bacterial communities in the phylloplane of Prunus species – Yeonhwa Jo – Journal of Basic Microbiology

Changes in rhizospheric microbial community structure and function during the natural recovery of abandoned cropland on the Loess Plateau, China – Chao Zhang – Ecological Engineering

Climate-induced die-off affects plant–soil–microbe ecological relationship and functioning – Francisco Lloret – FEMS Microbiology Ecology

Leaf-inhabiting endophytic yeasts are abundant but unevenly distributed in three Ficus species from botanical garden greenhouses in Germany – Michael Jay L. Solis – Mycological Progress

Soil and sediment microbiome

Succession of Bacterial Community Structure and Diversity in Soil along a Chronosequence of Reclamation and Re-Vegetation on Coal Mine Spoils in China – Yuanyuan Li – PLOS ONE

Soil microbial communities identify organic amendments for use during oil sands reclamation – M.L. Béass – Ecological Engineering

Forest canopy structural controls over throughfall affect soil microbial community structure in an epiphyte-laden maritime oak stand – Carl Rosier – Ecohydrology

Pyrosequencing revealed highly microbial phylogenetic diversity in ferromanganese nodules from farmland – Min Hu – Environ Sci Processes Impacts

Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage – Björn Breidenbach1 and Ralf Conrad – Frontiers in Microbiology

Variations of Bacterial Community Structure and Composition in Mangrove Sediment at Different Depths in Southeastern Brazil – Lucas William Mendes – Diversity

Invasive dreissenid mussels and benthic algae in Lake Michigan: characterizing effects on sediment bacterial communities – Philip O. Lee – FEMS Microbiology Ecology

Plant assemblage composition and soil P concentration differentially affect communities of AM and total fungi in a semi-arid grassland – Rim Klabi – FEMS Microbiology Ecology

Bacterial and Archaeal Communities in Sediments of the North Chinese Marginal Seas
Jiwen Liu – Microbial Ecology

Microbial community composition and diversity in Caspian Sea sediments – Nagissa Mahmoudi – FEMS Microbiology Ecology

Priming of the decomposition of ageing soil organic matter: concentration dependence and microbial control – Johannes Rousk – Functional Ecology

Influence of spoil type on afforestation success and natural vegetative recolonization on a surface coal mine in Appalachia, United States – Kenton Sena – Restoration Ecology

Water microbiome

Bacterial community responses to a gradient of alkaline mountaintop mine drainage in Central Appalachian streams – Raven L Bier – The ISME Journal

Big answers from small worlds: a user’s guide for protist microcosms as a model system in ecology and evolution – Florian Altermatt – Methods in Ecology and Evolution

Spatial scales of bacterial community diversity at cold seeps (Eastern Mediterranean Sea) – Petra Pop Ristova – ISME Journal

The effects of oil pollution on Antarctic benthic diatom communities over 5 years – R. Polmear – Marine Pollution Bulletin

Bacterial community dynamics in a swine wastewater anaerobic reactor revealed by 16S rDNA gene sequence analysis – An-Chi Liu – Journal of Biotechnology

Food microbiology

Antimicrobial activity of hop extracts against foodborne pathogens for meat applications – B. Kramer – Journal of Applied Microbiology

Molecular and enological characterization of Touriga Nacional non-Saccharomyces yeasts – Andreia Teixeira – Journal of Applied Microbiology

Metabolomics

Intra- and inter-species interactions in microbial communities – Luis R. Comolli – Frontiers in Microbiology

Metabolomic Pattern Analysis after Mediterranean Diet Intervention in a Nondiabetic Population: A 1- and 3-Year Follow-up in the PREDIMED Study – Rosa Vázquez-Fresno – Journal of Proteome Research

A gut microbial metabolite of linoleic acid, 10-hydroxy-cis-12-octadecenoic acid, ameliorates intestinal epithelial barrier impairment partially via GPR40/MEK-ERK pathway – Junki Miyamoto – The Journal of Biological Chemistry

Bioinformatics

IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries – Patricio Jeraldo – PLOS ONE

Techniques

Normalization of environmental metagenomic DNA enhances the discovery of under-represented microbial community members – Jean-Baptiste Ramond – Letters in Applied Microbiology

Remediation of pharmaceuticals and personal care products using an aerobic granular sludge sequencing bioreactor and microbial community profiling using Solexa sequencing technology analysis – Xia Zhao – Bioresource Technology

Predicting Bacterial Community Assemblages Using an Artificial Neural Network Approach – Peter Larsen – Artificial Neural Networks

Functional foods

Systematic review of randomized controlled trials of probiotics, prebiotics, and synbiotics in inflammatory bowel disease – Ghouri YA – Clinical and Experimental Gastroenterology

More microbiology

Life in a World without Microbes – Jack A. Gilbert, Josh D. Neufeld – PLOS Biology

Demystifying Escherichia coli pathovars – Kate S. Baker – Nature Reviews Microbiology

Wolbachia small noncoding RNAs and their role in cross-kingdom communications – Jaime G. Mayoral – PNAS USA

How the virophage compels the need to readdress the classification of microbes – Didier Raoult – Virology

Microbes in the news

To Get To The Bottom Of Your Microbiome, Start With A Swab Of Poo – Katherine Harmon Courage – NPR Shots Health News

Seth Bordenstein: Expert to give talk on animal microbiome – Arizona State University

Could a bacterial ‘fingerprint’ solve a sexual assault case? – Rachel Feltman – Washington Post

Oil-Dwelling Bacteria Are Highly Social Creatures, Contrary To Previous Belief – Rebekah Marcarelli – Headlines and Global News

Methane Bursts On Mars Could Hint At Previous Life – Joe Palca – NPR

Bik’s Picks

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping – Suhas S.P. Rao – Cell

Shift workers ‘sicker and fatter’ – James Gallagher – BBC News

How to turn 4,000 watts of white light into a 45-meter-wide rainbow – Popular Science

How to Bike Home Your Christmas Tree in 11 Simple Steps – Anna Broadway – City Lab

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December 12, 2014

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Human oral microbiome

Periodontal microbiology in Latin America – Adolfo Contreras – Periodontology 2000

Current perspective of the impact of smoking on the progression and treatment of periodontitis – Francisco H. Nociti Jr – Periodontology 2000

Effect of periodontal treatment on preterm birth rate: a systematic review of meta-analyses – Néstor J. López, Sergio Uribe and Benjamín Martinez – Periodontology 2000

Pregnancy and birth

* The Infant Microbiome Development: Mom Matters – Noel T. Mueller – Trends in Molecular Medicine

(see also above) Effect of periodontal treatment on preterm birth rate: a systematic review of meta-analyses – Néstor J. López, Sergio Uribe and Benjamín Martinez – Periodontology 2000

Pre- and probiotics, functional foods

Repeated cooking and freezing of whole wheat flour increases resistant starch with beneficial impacts on in vitro fecal fermentation properties – Jennifer A. Arcila, Devin J. Rose – Journal of Functional Foods

Potential of cereal grains and grain legumes in modulating pigs’ intestinal microbiota – A review – Tobias Aumiller – Livestock Science

Significance of Inulin Fructans in the Human Diet – Gertjan Schaafsma and Joanne L. Slavin – Comprehensive Reviews in Food Science and Food Safety

Effects of targeted delivery of propionate to the human colon on appetite regulation, body weight maintenance and adiposity in overweight adults – Edward S Chambers – Gut

Animal models

P47 – A dietary-driven redox modulation of gut microbiome-host interactions: the rescue of epithelial barrier and mucus production during dysbiosis by dietary nitrate – Bárbara Rocha – Free Radical Biology and Medicine

Dietary Pectin–Derived Acidic Oligosaccharides Improve the Pulmonary Bacterial Clearance of Pseudomonas aeruginosa Lung Infection in Mice by Modulating Intestinal Microbiota and Immunity – Henry Bernard – The Journal of Infectious Diseases

Soil microbiome

Response of autochthonous microbiota of diesel polluted soils to land-farming treatments – Gloria Andrea Silva-Castro – Environmental Research

Are there links between responses of soil microbes and ecosystem functioning to elevated CO2, N deposition and warming? A global perspective – Pablo García-Palacios – Global Change Biology

Experimental evaluation of CO2 percolation effects on subsurface soil microbiota –
Patricia Österreicher-Cunha – International Journal of Greenhouse Gas Control

Water microbiome

In situ grazing experiments apply new technology to gain insights into deep-sea microbial food webs – Maria G. Pachiadaki – Deep Sea Research Part II: Topical Studies in Oceanography

Metabolomics

Microbial Urease in Health and Disease – Diego Mora, Stefania Arioli – PLOS Pathogens

Bioinformatics

“Bioinformatics: Introduction and Methods,” a Bilingual Massive Open Online Course (MOOC) as a New Example for Global Bioinformatics Education – Yang Ding – PLOS Computational Biology

Techniques
Effect of Two Different Commercial DNA Extraction Kits on the Bacterial 16S rRNA gene Denaturing Gradient Gel Electrophoresis Profile of Arabian Gelding Feces – Megan L. Shepherd – Journal of Equine Veterinary Science

More microbiology papers

mBio Addresses the Pause in Gain-of-Function (GOF) Experiments Involving Pathogens with Pandemic Potential (PPP) – Arturo Casadevall – mBio

The battle for iron – Andrew E. Armitage, Hal Drakesmith – Science

Bacteriophage exclusion, a new defense system – Rodolphe Barrangou and John van der Oost – The EMBO Journal

Microbes in the news

Poo And You: A Journey Into The Guts Of A Microbiome – Katherine Harmon Courage – NPR Health

The Gut and Arthritis: The Evidence Grows – Nancy Walsh and Diana Swift – MedPageToday

Gross! Apparently Your Bacteria Is What Makes or Breaks a Relationship? – Zahra Barnes – Glamour.com (who knew?)

A Powder Made From Bacteria Waste Could Curb Overeating – Sarah Zhang – Gizmodo

Science, publishing, career

Scientific Elevator Pitches: A number of competitions around the world are challenging young scientists to describe their research in mere minutes – Rina Shaikh-Lesko – The Scientist

More science doctorates, fewer postdoctorate science jobs – Beryl Lieff Benderly – Science Careers

Making science a desirable career – Jessica K. Polka, Kristin A. Krukenberg – Science Magazine

Tips for Talking to Politicians: Members of an American Society for Cell Biology panel urge their colleagues to consider science advocacy – Tracy Vence – The Scientist

What Should High School Students Learn About Science? – Ria Misra – Space io9

Faculty member leads development of webinars that improve science education – Samantha Schwartz – PennState News

In defamation case, PubPeer moves to quash subpoena to unmask anonymous commenters – Kelly Servick – Science Magazine

Scientific American’s Top 10 Science Stories of 2014 – Scientific American

Bik’s Picks

Why whale poo matters – George Monbiot – The Guardian

Introduction to special Science Issue on bird genomes: A flock of genomes – Guojie Zhang – Science

The Darwin Awards: sex differences in idiotic behaviour – Ben Alexander Daniel Lendrem – British Medical Journal

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December 11, 2014

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The Bay Area is getting drenched with rain right now, and several leaks in our roof kept me busy with buckets and towels, but the power is still on, so here we go:

Human microbiome general

* Review: The demographic determinants of human microbiome health – Sylvie Estrela – Trends in Microbiology

Human oral microbiome

Salivary Mucins Protect Surfaces from Colonization by Cariogenic Bacteria – Erica Shapiro Frenkel – Applied and Environmental Microbiology

Human gut microbiome

* Effects of the gut microbiota on bone mass – Claes Ohlsson, Klara Sjögren – Trends in Endocrinology & Metabolism

Discovery of a Conjugative Megaplasmid in Bifidobacterium breve – Francesca Bottacini – Applied and Environmental Microbiology

Microbiome of pregnancy and birth

Microbiome of the placenta in pre-eclampsia supports the role of bacteria in the multifactorial cause of pre-eclampsia – Ranmalee Amarasekara – Journal of Obstetrics and Gynaecology Research
Animal and bioreactor models

Optimization of a rapid and efficient analytical pipeline for in-depth metaproteome characterization: evaluation on mock microbial mixtures and application to the mouse gut microbiome – Alessandro Tanca – Microbiome

* Microbial shifts in the aging mouse gut – Morgan GI Langille – Microbiome

Development of human colonic microbiota in the computer-controlled dynamic SIMulator of the GastroIntestinal tract SIMGI – Elvira Barroso – LWT – Food Science and Technology

Protocols for Microcosms for Growing Biofilms on Hydrophobic Substrates: A Polyphasic Approach to Study Biodiversity, Metabolic Activity, and Biofilm Architecture – Wolf-Rainer Abraham – Springer Protocols Handbooks 2014

Animal microbiome

Acidobacteria appear to dominate the microbiome of two sympatric Caribbean Sponges and one Zoanthid – Aileen O¿Connor-Sánchez – Biological Research

Plant microbiome

The impact of systemic and copper pesticide applications on the phyllosphere microflora of tomatoes – Andrea R Ottesen – Journal of the Science of Food and Agriculture

Soil and sediment microbiome

Linkages between the soil organic matter fractions and the microbial metabolic functional diversity within a broad-leaved Korean pine forest – Jing Tian – European Journal of Soil Biology

Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests – Karina E. Clemmensen – New Phytologist

Comparison of bacterial succession in green waste composts amended with inorganic fertiliser and wastewater treatment plant sludge – Sean Storey – Bioresource Technology

Water microbiome

Initial community and environment determine the response of bacterial communities to dispersant and oil contamination – Alice C. Ortmann – Marine Pollution Bulletin

Initial community and environment determine the response of bacterial communities to dispersant and oil contamination – Alice C. Ortmann, YueHan Lu – Marine Pollution Bulletin

Protistan diversity in a permanently stratified meromictic lake (Lake Alatsee, SW Germany) – Andreas Oikonomou – Environmental Microbiology

Exploration of Microbial Diversity of Taptapani (India) Hot Spring Through Molecular Phylogenetic Analysis – Sudip Kumar Sen – Arabian Journal for Science and Engineering

Food microbiology

Selection of Autochthonous Strains as Starter Cultures for Fermented Fish Products – Barbara Speranza – Journal of Food Science

Microbes in the news

Pregnancy Germs: Friend Or Foe? – How The Maternal Microbiome Influences Pregnancy Health – PR NewsWire / March of Dimes

Study Hints Gut Microbiome Plays A Role in Multiple Sclerosis –
Kate O’Rourke – Gastroenterology and Endoscopy News

“The Great Plate Count Anomaly” that is no more – Gemma Reguera – Small Things Considered ASM

Google Science Fair – Bacteria boosting cereal crop yields – Brett Worthington – ABC Net Australia

Guts of obese dogs look similar to those of obese people – Agata Blaszczak-Boxe – Science Magazine

Baby infected in birthing pool died of Legionnaire’s disease – Bahar Gholipour – CBS News

Science, publishing, and career

Scientists Often Skip A Simple Test That Could Verify Their Work – NPR Morning Edition

Study of massive preprint archive hints at the geography of plagiarism – John Bohannon – Science Insider

Bik’s Picks

Deep Neural Networks are Easily Fooled: High Confidence Predictions for Unrecognizable Images – Anh Nguyen – Arxiv

Three-in-one drug cuts body weight by a third – Nsikan Akpan – Science Magazine

Water vapor on Rosetta’s target comet significantly different from that found on Earth – Science Daily

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December 10, 2014

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Food microbiome

The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types – Jenna M. Lang – PeerJ

Human oral microbiome

Subgingival microbial profiles of Sudanese patients with aggressive periodontitis – H. R. Z. Elabdeen – Journal of Periodontal Research

Human bladder microbiome

Interplay between Bladder Microbiota and Urinary Antimicrobial Peptides: Mechanisms for Human Urinary Tract Infection Risk and Symptom Severity – Vanessa Nienhouse – PLOS ONE

Human gut microbiome

Immunomodulatory Properties of Streptococcus and Veillonella Isolates from the Human Small Intestine Microbiota – Bartholomeus van den Bogert – PLOS ONE

Animal models of microbiome research

The Gut Commensal Bacteroides thetaiotaomicron Exacerbates Enteric Infection through Modification of the Metabolic Landscape – Meredith M. Curtis – Cell Host & Microbe

Gut Microbiota-Produced Succinate Promotes C. difficile Infection after Antibiotic Treatment or Motility Disturbance – Jessica A. Ferreyra – Cell Host & Microbe

Regionally Distinct Alterations in the Composition of the Gut Microbiota in Rats with Streptozotocin-Induced Diabetes – Roland Wirth – PLOS ONE

Animal microbiome

Environmentally Determined Differences in the Murine Lung Microbiota and Their Relation to Alveolar Architecture – Yeojun Yun – PLOS ONE

Bacteria and Methanogens Differ along the Gastrointestinal Tract of Chinese Roe Deer (Capreolus pygargus) – Zhipeng Li – PLOS ONE

Transcriptomic Immune Response of the Cotton Stainer Dysdercus fasciatus to Experimental Elimination of Vitamin-Supplementing Intestinal Symbionts – Eugen Bauer – PLOS ONE

Metabolomics

Stool Phospholipid Signature is Altered by Diet and Tumors – Julie M. Davies – PLOS ONE

Pathogens’ Exploitation of the Intestinal Food Web
Tu Anh Pham N., Trevor D. Lawley – Cell Host & Microbe

Could resistant starch be the redeemer of dietary carbohydrate? – M Denise Robertson – Practical Diabetes

A New Insight into the Physiological Role of Bile Salt Hydrolase among Intestinal Bacteria from the Genus Bifidobacterium – Piotr Jarocki – PLOS ONE

Metagenomics

Maths on microbes: adding microbial ecophysiology to metagenomics – Wilfred F. M. Röling – Microbial Biotechnology

Functional optimization of gene clusters by combinatorial design and assembly – Michael J Smanski – Nature Biotechnology

More microbiology

Microbiology: Ditch the term pathogen – Arturo Casadevall & Liise-anne Pirofski – Nature

New sequencing technique: MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island – Philip M Ashton – Nature Biotechnology

Microbes in the news

NASA ISS On-Orbit Status 5 December 2014: Microbiome Experiment – SpaceRef

Bacteria’s Game of ‘Telephone’ Foils Microbiologists’ Eavesdropping – Kim Krieger – UConnToday

Science, publishing, career

The Point When Science Becomes Publicity – James Hamblin – The Atlantic

No Lovin’ Feeling… for Science Fair – Claire Wapole – Huffington Post

How to cope when things go wrong in academia – Julie Gould – Nature Jobs

Scientific Peer Review Is Broken. We’re Fighting to Fix It With Anonymity – The Founders of PubPeer – Wired.com

Not sure how old this is, but I liked the graph: The illustrated guide to a Ph.D. – Matt Might

Ocean biology: Marine dreams – Chris Woolston – Nature

New postdoc report covers familiar ground – Beryl Lieff Benderly, Jim Austin – Science Careers

Bik’s Picks

Injectable 3-D vaccines could fight cancer, infectious diseases – ScienceDaily

Glittering Nobel Gown Represents Scientist’s Work – Joanne Manaster – Scientific American

This Commuter Bus Runs On Poop- A U.K.-based biogas plant has developed a 40-seater than runs on converted sewage and food waste – Corinne Iozzio – Smithsonian

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December 9, 2014

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Human oral microbiome

* Characterization and comparison of bacterial communities in benign vocal fold lesions – Alissa S Hanshew – Microbiome

Bacterial invasion and persistence: critical events in the pathogenesis of periodontitis? – S. Ji – Journal of Periodontal Research

Human skin microbiome

This took two years to publish, but here it is: Meeting report for the 1st skin microbiota workshop, Boulder, CO October 15-16 2012 – Jack A Gilbert – Standards in Genomic Sciences

Human respiratory microbiome

Assessment of Airway Microbiota and Inflammation in Cystic Fibrosis Using Multiple Sampling Methods – Edith T. Zemanick – Annals of the American Thoracic Society

Human gut microbiome

* Stability of Gut Enterotypes in Korean Monozygotic Twins and Their Association with Biomarkers and Diet – Mi Young Lim – Scientific Reports

* Microbiota organization is a distinct feature of proximal colorectal cancers – Christine M. Dejea – PNAS USA

Review: Crosstalk between intestinal microbiota, adipose tissue and skeletal muscle as an early event in systemic low-grade inflammation and the development of obesity and diabetes – Christian Bleau – Diabetes/Metabolism Research and Reviews

Pathophysiological responses from human gut microbiome – Anindya Roy Chowdhury, Utpal Bakshi – World Journal of Translational Medicine

Animal models of microbiome research

Microbiome-metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model – Sheng-yong Mao – Environmental Microbiology

Animal microbiome

Carpoglyphus lactis (Acari: Astigmata) from various dried fruits differed in associated microorganisms – Jan Hubert – Journal of Applied Microbiology

Bacterial dynamics within the mucus, tissue and skeleton of the coral Porites lutea during different seasons – Jie Li – Scientific Reports

 

Investigation of biotechnological potential of sponge-associated bacteria collected in Brazilian coast – O.C.S. Santos – Letters in Applied Microbiology

Plant microbiome

* Removal of floral microbiota reduces floral terpene emissions – Josep Peñuelas – Scientific Reports

Contrasting diversity of epibiotic bacteria and surrounding bacterioplankton of a common submerged macrophyte, Potamogeton crispus, in freshwater lakes – Dan He – FEMS Microbiology Ecology

Review: Sphagnum physiology in the context of changing climate: emergent influences of genomics, modelling and host–microbiome interactions on understanding ecosystem function – David J. Weston – Plant, Cell & Environment

Book: Principles of Plant-Microbe Interactions – Springer

Soil and sediment microbiome

Anthropogenic land use shapes the composition and phylogenetic structure of soil arbuscular mycorrhizal fungal communities – Mari Moora – FEMS Microbiology Ecology

Halophyte plant colonization as a driver of the composition of bacterial communities in salt marshes chronically exposed to oil hydrocarbons – Vanessa Oliveira – FEMS Microbiology Ecology

Changes in microbial communities in coastal sediments along natural CO2 gradients at a volcanic vent in Papua New Guinea – Felix F. Raulf – Environmental Microbiology

Nitrogen Cycling Processes and Microbial Community Composition in Bed Sediments in the Yukon River at Pilot Station – Deborah A. Repert – Journal of Geophysical Research: Biogeosciences

Soil bacterial and fungal communities respond differently to various isothiocyanates added for biofumigation – Ping Hu – Frontiers in Microbiology

Primary succession of soil enzyme activity and heterotrophic microbial communities along the chronosequence of Tianshan Mountains No. 1 Glacier, China – Jun Zeng – Antonie van Leeuwenhoek

Water microbiome

Off-site impacts of agricultural composting: role of terrestrially derived organic matter in structuring aquatic microbial communities and their metabolic potential – Thomas Pommier – FEMS Microbiology Ecology

Microbiome of the built environment

* Diversity of Bacterial Communities of Fitness Center Surfaces in a U.S. Metropolitan Area – Nabanita Mukherjee – International Journal of Environmental Research and Public Health

Food microbiology

Potentially probiotic acetic acid bacteria isolation and identification from traditional dairies microbiota – Babak Haghshenas – International Journal of Food Science & Technology

Metagenomics

Microbial community pattern detection in human body habitats via ensemble clustering framework – Peng Yang – BMC Systems Biology

Proteomics and metabolomics

Insights on the human microbiome and its xenobiotic metabolism: what is known about its effects on human physiology? – Tewes Tralau – Expert Opinion on Drug Metabolism & Toxicology

Proteomic tools to decipher microbial community structure and functioning – Florence Arsène-Ploetze – Environmental Science and Pollution Research

Systems-based approaches to unravel multi-species microbial community functioning – Florence Abram – Computational and Structural Biotechnology Journal

Amplification and other techniques

* Multi-template polymerase chain reaction – Elena Kalle – Biomolecular Detection and Quantification

Microfluidic static droplet array for analyzing microbial communication on a population gradient – Heon-Ho Jeong – Lab Chip

More microbiology papers

* Gain-of-function experiments: time for a real debate – W. Paul Duprex (with David Relman) – Nature Reviews Microbiology

Ciprofloxacin mechanism: Emergence of antibiotic resistance from multinucleated bacterial filaments – Julia Bos – PNAS USA

Microbes in the news

The fragrance of flowers depends on the fungi and bacteria that coated – Beta Wired

The Human Microbiome: Getting Personal – Katy Califf – ASM Microbe

Science, publishing, career

Scientists Are Not That Smart – Chad Orzel – New York Magazine

io9 Science Survey: Tell Us About Working With Rodents in the Lab – Annalee Newitz – io9

Best Way for Professors to Get Good Student Evaluations? Be Male – Amanda Marcotte – Slate

Bik’s Picks

Unfortunately sold out, but really cute: DNA Molecule Plush – ThinkGeek

The birth of a dinosaur footprint: Subsurface 3D motion reconstruction and discrete element simulation reveal track ontogeny (with movies) – Peter L. Falkingham – PNAS USA

Billionaire’s New Science Institute Plans “Google Maps” View of Cells – Joshn Fischman – Scientific American

Expanded DNA alphabet wins Science award – Bradley J. Fikes – UT San Diego

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Microbiome digest, December 8, 2014

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Human microbiome general

The human microbiome: opportunities and challenges for clinical care – Geraint B. Rogers – Internal Medicine Journal

Evaluative Profiling of Arsenic Sensing and Regulatory Systems in the Human Microbiome Project Genomes – Raphael D Isokpehi – Microbiology Insights

Human oral microbiome

* High resolution taxonomic profiling of the subgingival microbiome for biomarker discovery and periodontitis diagnosis – Szymon P. Szafranski – Applied and Environmental Microbiology

Human gut microbiome

Crosstalk at the mucosal border: importance of the gut microenvironment in IBS – Lena Öhman – Nature Reviews Gastroenterology & Hepatology

Antimicrobial resistance characteristics and fitness of Gram negative faecal bacteria from volunteers treated with minocycline or amoxicillin – Miranda Kirchner – Frontiers in Microbiology

Decrease in lactobacilli in the intestinal microbiota of celiac children with a gluten-free diet, and selection of potentially probiotic strains – María J. Lorenzo Pisarello – Canadian Journal of Microbiology

Safety assessment of genetically modified rice expressing human serum albumin from urine metabonomics and fecal bacterial profile – Xiaozhe Qi – Food and Chemical Toxicology

Pregnancy and birth microbiome

Placental Microbiome and Its Role in Preterm Birth – Bin Cao – NeoReviews

High A. vaginae and G. vaginalis vaginal loads are associated with preterm birth – Florence Bretelle – Clinical Infectious Diseases

Cesarean Section and Chronic Immune Disorders – Astrid Sevelsted – Pediatrics

Animal and other models of microbiome research

Intestinal epithelial ​MyD88 is a sensor switching host metabolism towards obesity according to nutritional status – Amandine Everard – Nature Communications

Bugs and Food: A Recipe for Cancer? – Christina L. Ohland, Christian Jobin – Cell Metabolism

The current provided by oxygen-reducing microbial cathodes is related to the composition of their bacterial community – Mickaël Rimboud – Bioelectrochemistry

Animal microbiome

The putative functional ecology and distribution of archaeal communities in sponges, sediment and seawater in a coral reef environment – Ana R.M. Polónia – Molecular Ecology

Plant microbiome

* The role of bacteria and mycorrhiza in plant sulfur supply – Jacinta M. Gahan and Achim Schmalenberger – Frontiers in Plant Science

Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation – Sunil Mundra – New Phytologist

Soil and sediment microbiome

Impacts of altered precipitation regimes on soil communities and biogeochemistry in arid and semi-arid ecosystems – Uffe N. Nielsen – Global Change Biology

* Effects of tree identity dominate over tree diversity on the soil microbial community structure – Andrea Scheibe – Soil Biology and Biochemistry

Smooth brome invasion increases rare soil bacterial species prevalence, bacterial species richness and evenness – Candace L. Piper – Journal of Ecology

The interactive effects of elevated ozone and wheat cultivars on soil microbial community composition and metabolic diversity – Xuelian Bao – Applied Soil Ecology

Seasonal variations of the composition of microbial biofilms in sandy tidal flats: Focus of fatty acids, pigments and exopolymers – Claire Passarelli – Estuarine, Coastal and Shelf Science

Pharmaceuticals in the environment: Biodegradation and effects on natural microbial communities. A Review – Anna Barra Caracciolo – Journal of Pharmaceutical and Biomedical Analysis

Water microbiome

Successional Change in Microbial Communities of Benthic Phormidium-Dominated Biofilms – Katie A. Brasell – Microbial Ecology

Microbiome of the built environment

Characterizing airborne fungal and bacterial concentrations and emission rates in six occupied children’s classrooms – D. Hospodsky – Indoor Air

Food microbiology

Analysis of the bacterial community in aged and aging pit mud of Chinese Luzhou-flavour liquor by combined PCR-DGGE and quantitative PCR assay – Huipeng Liang – Journal of the Science of Food and Agriculture

Phages and viruses

Emerging methods to study bacteriophage infection at the single-cell level – Vinh T. Dang and Matthew B. Sullivan – Frontiers in Microbiology

Metabolomics

* The Community Ecology of Microbial Molecules – Robert A. Quinn, Theodore Alexandrov – Journal of Chemical Ecology

Ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry for rapid analysis of the metabolites of morroniside produced by human intestinal bacteria – Min Zhao – Journal of Chromatography B

Small-intestinal or colonic microbiota as a potential amino acid source in animals – Werner G. Bergen – Amino Acids

Techniques

Comparative assessment of next-generation sequencing, denaturing gradient gel electrophoresis, clonal restriction fragment length polymorphism and cloning-sequencing as methods for characterizing commercial microbial consortia – A.D. Samarajeewa – Journal of Microbiological Methods

Microbes in the news

Now We Know Some Creepy Things About How Penicillin Destroys Bacteria – Esther Inglis-Arkell – IO9

Arctic bacteria converts mercury – Kristian Sjøgren – ScienceNordic

Should I Eat Greek Yogurt? – Mandy Oaklander – Time

CSU team examines dairy-cattle microorganisms to improve food safety – Kristen Browning-Blas – Bovine Vet Online

Glyphosate used with GMO crops under attack for disrupting microbiome: Science or a gut feeling? – David Warmflash – Genetic Literacy Project

#BacteriaHysteria: Why it’s time to detox your desk: Average worker comes into contact with more than 10 MILLION disease-causing bacteria lurking on their keyboard, phone and mouse – Lizzie Parry – Daily Mail

Bik’s Picks

The Yearbook: Our list of newsmakers this year – Manasi Vaidya & Shraddha Chakradhar – Nature Medicine

Notable advances 2014 – Amanda Keener – Nature Medicine

Let’s face it, for robots, falling down is easy. But how do you teach them to land safely? – Maki Naro – Popular Science

Force-feeding a human to a snake is not science (and is also super dumb) – Rachel Feltman – Washington Post

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Microbiome Digest, December 5, 2014

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Human oral microbiome

* Noma Affected Children from Niger Have Distinct Oral Microbial Communities Based on High-Throughput Sequencing of 16S rRNA Gene Fragments – Katrine L. Whiteson – PLOS Neglected Tropical Diseases

* Ancient DNA analysis of dental calculus – Laura S. Weyrich – Journal of Human Evolution

Human gut microbiome

* Gut microbiota are related to Parkinson’s disease and clinical phenotype – Filip Scheperjans – Movement Disorders

The role of the microbiome in immune cell development – Nita H. Salzman – Annals of Allergy, Asthma & Immunology

Ezakiella peruensis gen. nov., sp. nov. isolated from human fecal sample from a coastal traditional community in Peru – Nisha B. Patel – Anaerobe

Microbiome and Immunology

Microbial Programming of Systemic Innate Immunity and Resistance to Infection – Thomas B. Clarke – PLOS Pathogens

Animal models of microbiome research

* (see also Metabolomics) Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome – Amir Zarrinpar – Cell Metabolism

Effects of cyclophosphamide on immune system and gut microbiota in mice – Xiaofei Xu, Xuewu Zhang – Microbiological Research

Gut microbiota and environment in patients with major burns – A preliminary report – Kentaro Shimizu – Burns

Animal microbiome

* The Feline Oral Microbiome: A Provisional 16S rRNA gene based Taxonomy with Full-length Reference Sequences – Floyd E. Dewhirst – Veterinary Microbiology

Diversity and health status specific fluctuations of intrauterine microbial communities in postpartum dairy cows – K. Wagener – Veerinary Microbiology

* Evidence of Polyethylene Biodegradation by Bacterial Strains from the Guts of Plastic-Eating Waxworms – Jun Yang – Environmental Science & Technology

Metabolomics

* Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome – Amir Zarrinpar – Cell Metabolism

A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis – Marnix H. Medema – PLOS Computational Biology

The Evolution of Fungal Metabolic Pathways – Jennifer H. Wisecaver – PLOS Genetics

The microbial degradation of onion flavonol glucosides and their roasting products by the human gut bacteria Eubacterium ramulus and Flavonifractor plautii – Katrin Ulbrich – Food Research International

Desulfovibrio desulfuricans isolates from the gut of a single individual: Structural and biological lipid a characterization – Wei Zhang-Sun – FEBS Letters

Metagenomics

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies – James F. Denton – PLOS Computational Biology

Microbes in the news

A Worm’s Gut Could Help Dispose of Plastic Trash: Microbes found in the guts of waxworms like to feast on polyethylene – Rachel Nuwer – Smithsonian Magazine

Friendly bacteria are protective against malaria – MedicalXpress

Self-healing Concrete Vanishes Potholes Using Bacteria. Here’s How it Works – Jan Dizon – TechTimes

Wireless Implant Eliminates Bacteria, Then Dissolves – WND

Science, publishing and career

* Ten Simple Rules for Finishing Your PhD – Jacopo Marino – PLOS Computational Biology

Bik’s Picks

Amid Bugs, Hail, Floods and Bacteria, Italian Olives Take a Beating – Elisabetta Povoledo – New York Times

See it, touch it, feel it: Researchers use ultrasound to make invisible 3-D haptic shape that can be seen and felt – Science Daily

Satire: Breaking: James Watson Faked Winning A Nobel Prize – The Allium

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